[Prevalence of the GA risk haplotype of the rs1554483 and rs4864548 polymorphisms of the CLOCK gene associated with obesity and overweight in 26 populations]. / Prevalencia del haplotipo de riesgo GA de los polimorfismos rs1554483 y rs4864548 del gen CLOCK asociados a la obesidad y el sobrepeso en 26 poblaciones.

Introduction: Introduction: the GA haplotype of polymorphisms rs1554483 and rs4864548 has been associated with components of the metabolic syndrome such as high blood pressure and triglyceride levels; its carriers have a risk of obesity, 1.5 times higher than the rest of the population. Methodology: SNP rs1554483 and rs4864548 were obtained from 2504 individuals from the "1000genomes phase 3" database. Data were grouped into five macro populations (Africa, East Asia, South Asia, Europe and Latin America) covering a total of 26 populations. Differences in haplotype frequency between macro populations and populations were analyzed, for which Fisher's F statistic was used. Results: the macro population of Africa presented the lowest frequency (17.9 %) and that of East Asia the highest (57.4 %). Within the populations there is a relative homogeneity in the frequencies, except in the case of those that make up the macro population of Latin America where the Peruvian population of Lima and the Puerto Rican population present much higher frequencies than the rest. Conclusions: the GA haplotype presents heterogeneity between macro populations, which suggests highly differentiated micro evolutionary processes between continents. We propose to study the association of the GA haplotype with other polymorphisms such as rs3749474, rs11932595 and rs6859524 that have also been associated with risk of obesity and factors associated with metabolic syndrome.

Introducción: Introducción: el haplotipo GA de los polimorfismos rs1554483 y rs4864548 se ha asociado con componentes del síndrome metabólico como la hipertensión arterial y los niveles de triglicéridos. Sus portadores presentan un riesgo de obesidad 1,5 veces mayor que el resto de la población. Metodología: se obtuvieron los SNP rs1554483 y rs4864548 de 2504 individuos desde la base de datos "1000genomes phase 3". Los datos se agruparon en cinco macropoblaciones (África, Asia Oriental, Asia Meridional, Europa y Latinoamérica) cubriendo un total de 26 poblaciones. Se analizaron las diferencias en la frecuencia del haplotipo entre las macropoblaciones y las poblaciones, para lo cual se utilizó el estadístico F de Fisher. Resultados: la macropoblación de África presentó la menor frecuencia (17,9 %) y la del Este de Asia la mayor (57,4 %). Dentro de las poblaciones existe una relativa homogeneidad en las frecuencias, excepto en el caso de las que componen la macropoblación de Latinoamérica, donde la población peruana de Lima y la puertorriqueña presentan frecuencias mucho mayores que el resto. Conclusiones: el haplotipo GA presenta heterogeneidad entre las macropoblaciones, lo que sugiere procesos microevolutivos altamente diferenciados entre los continentes. Se propone estudiar la asociación del haplotipo GA con otros polimorfismos, como rs3749474, rs11932595 y rs6859524, que también se han asociado con el riesgo de obesidad y factores asociados al síndrome metabólico.

Imputation of SNPs associated with presbycusis through linkage disequilibrium analysis in the ILDR1 gene.

The single-nucleotide polymorphisms (SNP) ILDR1 rs2332035 has shown a high statistical association with presbycusis (hearing loss with age or age-related hearing impairment (ARHI)), according to genetic association studies in European populations. However, linked markers have not been surveyed. Here linkage disequilibrium (LD) of markers in ILDR1, in relation to rs2332035, is explored in the 2504 individuals from the 1000Genomes database. Of the 920 SNPs retrieved, 10 showed strong LD (r2= 0.8) in Europeans and Latin Americans, which are proposed here as candidate markers for both control-case association and cause-effect studies in both populations.

[Variability of the genetic marker CLOCK rs3749474 and its impact on research and clinical trials on obesity and circadian rhythm]. / Variabilidad del marcador genético CLOCK rs3749474 y su impacto en la investigación y ensayos clínicos sobre obesidad y ritmo circadiano.

Introduction: Introduction: circadian rhythms influence eating behavior, with the CLOCK gene being one of those responsible for its regulation. The rs3749474T/C of the CLOCK gene has been associated with an increased risk of obesity. Those who carry the T allele have greater weight loss on a diet low in carbohydrates and lipids than those who have the CC form. Methodology: using the 1000 Genomes database, the genotype of the single nucleotide polymorphism (SNP) rs3749474 was obtained from 2,504 individuals, covering five macro-populations (Africa, East Asia, South Asia, Europe and Latin America) and 26 populations. CT and TT were treated as non-risk genotypes and CC as risk. Fisher's exact test was used to compare the frequencies of risk and non-risk genotypes among the five macro populations. Results: there is a high differentiation for the frequency of genotypes carrying the T allele among the macro-populations: Africa reached only 31.47 %, Europe 56.86 %; Latin America 66.28 %; South Asia 68.3 % and East Asia 81.15 %, with significant differences (pFisher < 0.05) in all comparisons, except between Latin America and South Asia. Low heterogeneity was observed between populations within each macro population. Conclusions: the high heterogeneity for the genotypic frequencies of CLOCK rs3749474 in the studied macro-populations indicates that the decrease in the consumption of carbohydrates and lipids will have a heterogeneous impact, from the epidemiological point of view. This suggests including the genetic ancestry in later studies of association between circadian cycles, eating behavior and obesity, in order to develop personalized clinical tests.

Introducción: Introducción: los ritmos circadianos influyen en la conducta alimentaria, siendo el gen CLOCK uno de los encargados de su regulación. El rs3749474T/C del gen CLOCK ha sido asociado a un mayor riesgo de obesidad y quienes portan el alelo T presentan una mayor pérdida de peso ante una dieta baja en carbohidratos y lípidos que quienes poseen la forma CC. Material y métodos: usando la base de datos 1000 Genomes se obtuvo el genotipo del polimorfismo de nucleótido único (SNP) rs3749474 de 2.504 individuos, abarcando cinco macropoblaciones (África, Este Asiático, Sur Asiático, Europa y Latinoamérica) y 26 poblaciones. CT y TT fueron tratados como genotipos de no riesgo y CC, como de riesgo. Se utilizó la prueba exacta de Fisher para comparar las frecuencias de los genotipos de riesgo y no riesgo. Resultados: existe una alta diferenciación para la frecuencia de genotipos portadores del alelo T entre las macropoblaciones: África alcanzó solo el 31,47 %; Europa, un 56,86 %; Latinoamérica, un 66,28 %; el Sur Asiático, un 68,3 %; y el Este Asiático, un 81,15 %, con diferencias significativas (pFisher < 0,05) en todas las comparaciones, excepto entre Latinoamérica y Sur Asiático. Se observó una baja heterogeneidad entre poblaciones dentro de cada macropoblación. Conclusiones: la alta heterogeneidad para las frecuencias genotípicas de CLOCK rs3749474 en las macropoblaciones estudiadas indica que la disminución del consumo de carbohidratos y lípidos tendrá un impacto heterogéneo desde el punto de vista epidemiológico. Esto sugiere incluir la ancestría genética en posteriores estudios de asociación entre ciclos circadianos, conducta alimentaria y obesidad, con el objeto de desarrollar pruebas clínicas personalizadas.

Signatures of positive selection on the hepatic lipase gene in human populations.

The hepatic lipase plays a central role in the lipid metabolism, catalyzing the hydrolysis of phospholipids, monoglycerides, diglycerides, and triglycerides, and acyl-CoA. It is also implied in the conversion of very low-density lipoprotein and intermediate density lipoprotein to low density lipoproteins. As a consequence, the gene encoding the hepatic lipase (LIPC) is associated with several diseases derived from the imbalance of lipids that are in general derived from the interaction between life styles and genetic architecture. Therefore, it is interesting to understand more about the characteristics of the microevolutionary processes affecting genes that, like LIPC, have a role in nutrition and lipid metabolism in human populations. We explored the selection signatures on LIPC in 26 populations, detecting three regions under recent positive selection.

Adaptation to milking agropastoralism in Chilean goat herders and nutritional benefit of lactase persistence.

The genetic trait of lactase persistence (LP) evolved as an adaptation to milking pastoralism in the Old World and is a well-known example of positive natural selection in humans. However, the specific mechanisms conferring this selective advantage are unknown. To understand the relationship between milk drinking, LP, growth, reproduction, and survival, communities of the Coquimbo Region in Chile, with recent adoption of milking agropastoralism, were used as a model population. DNA samples and data on stature, reproduction, and diet were collected from 451 participants. Lactose tolerance tests were done on 41 of them. The European -13,910*T (rs4988235) was the only LP causative variant found, showing strong association (99.6%) with LP phenotype. Models of associations of inferred LP status and milk consumption, with fertility, mortality, height, and weight were adjusted with measures of ancestry and relatedness to control for population structure. Although we found no statistically significant effect of LP on fertility, a significant effect (P = 0.002) was observed of LP on body mass index (BMI) in males and of BMI on fertility (P = 0.003). These results fail to support a causal relationship between LP and fertility yet suggest the idea of a nutritional advantage of LP. Furthermore, the proportion of European ancestry around the genetic region of -13,910*T is significantly higher (P = 0.008) than the proportion of European ancestry genome-wide, providing evidence of recent positive selection since European-Amerindian admixture. This signature was absent in nonpastoralist Latin American populations, supporting the hypothesis of specific adaptation to milking agropastoralism in the Coquimbo communities.

Lactase non-persistence and general patterns of dairy intake in indigenous and mestizo chilean populations.

OBJECTIVES: Lactase persistence (LP) is a genetic trait that has been studied among different countries and ethnic groups. In Latin America, the frequencies of this trait have been shown to vary according to the degree of admixture of the populations. The objective of this study is to better understand the relationship between this genetic trait and dairy intake in a multiethnic context through a synthesis of studies conducted in four regions of Chile. METHODS: Genotypes frequencies for the SNP LCT-13910C>T (rs4988235) and frequency of dairy consumption were obtained from four populations: Polynesians from Easter Island (Rapanui); Amerindians (Mapuche) and Mestizos from the Araucanía region; urban Mestizos from Santiago; and rural Mestizos from the Coquimbo region. Genetic differentiation and association between milk consumption and genotype frequencies were estimated. RESULTS: Genetic differentiation between Native and Mestizo populations was significant; the LP frequency in Mapuche and Rapanui was 10% and 25%, respectively, whereas among the Mestizos, LP frequency was near 40%. Dairy intake was below the nutritional recommendations for the four groups, and extremely below recommendations among the indigenous populations. Association between milk intake and LP was found in Santiago and Rapanui populations. CONCLUSIONS: Although the frequency of LP varies among the populations according to their degree of admixture, dairy consumption was very low across the populations. Given that the association between milk consumption and expected phenotype was found only in two of the populations analyzed, it seems that lactase non-persistence (LNP) is not the only cause for dairy avoidance. Thus, it is suggested that SES and cultural preferences are likely affecting dairy consumption.

[Alcohol consumption patterns and genotypes determining alcohol tolerance in Chilean university students]. / Patrones de consumo y genotipos determinantes de la tolerancia al alcohol: estudio en estudiantes universitarios de Santiago de Chile.

BACKGROUND: Alleles involved in inefficient (ADH1B2*2 and ALDH2*2) or efficient (SNP6, ADH4 gene) alcohol metabolism may influence the risk of alcoholism. Alcoholism susceptibility has been classified as protector and risk-dependence phenotypes, associated with inefficient and efficient alcohol genetic metabolizing variants, respectively. AIM: To investigate the possible association between genetic protective and risk-dependence variants and alcohol intake patterns. MATERIAL AND METHODS: Saliva DNA samples were obtained and the AUDIT (Alcohol Use Disorders Identification Test) questionnaire was applied to 210 university students aged between 18 and 25 years old. RESULTS: No statistically significant association between protective or risk-dependence genetic variants and alcohol pattern intake was detected. However, new categories of alcohol intake patterns-not included in the AUDIT questionnaire-were identified. CONCLUSIONS: No association between the protector and risk-dependence phenotypes and patterns of alcohol consumption was detected in this sample of students.

Patrones de consumo y genotipos determinantes de la tolerancia al alcohol: estudio en estudiantes universitarios de Santiago de Chile / Alcohol consumption patterns and genotypes determining alcohol tolerance in Chilean university students

Background: Alleles involved in inefficient (ADH1B2*2 and ALDH2*2) or efficient (SNP6, ADH4 gene) alcohol metabolism may influence the risk of alcoholism. Alcoholism susceptibility has been classified as protector and risk-dependence phenotypes, associated with inefficient and efficient alcohol genetic metabolizing variants, respectively. Aim: To investigate the possible association between genetic protective and risk-dependence variants and alcohol intake patterns. Material and Methods: Saliva DNA samples were obtained and the AUDIT (Alcohol Use Disorders Identification Test) questionnaire was applied to 210 university students aged between 18 and 25 years old. Results: No statistically significant association between protective or risk-dependence genetic variants and alcohol pattern intake was detected. However, new categories of alcohol intake patterns-not included in the AUDIT questionnaire-were identified. Conclusions: No association between the protector and risk-dependence phenotypes and patterns of alcohol consumption was detected in this sample of students.

Lactase persistence and dairy intake in Mapuche and Mestizo populations from southern Chile.

Lactase persistence (LP) occurs at a very low frequency in indigenous populations from Latin America, offering an opportunity to understand the relationship between this genetic trait and patterns of dairy consumption. Here, the frequency of LP is analyzed from Mapuche and -an adjacent- mestizo population inhabiting the Araucanía region. In addition to genotyping for LP, participants were surveyed in relation to general perception and consumption habits of dairy products. Low LP frequency (10%) and very low dairy intake was found among the Mapuche population as compared with Mestizo populations inhabiting Chile. The survey reported that the main reasons for avoidance of dairy were the gastrointestinal symptoms after dairy intake and cultural dietary habits. The interaction between low LP genotype frequency, low dairy intake, and sociocultural determinants is here discussed in the light of their potential health outcomes.

Fixations of the HIV-1 env gene refute neutralism: New evidence for pan-selective evolution.

We examined 103 nucleotide sequences of the HIV-1 env gene, sampled from 35 countries and tested: I) the random (neutral) distribution of the number of nucleotide changes; II) the proportion of bases at molecular equilibrium; III) the neutral expected homogeneity of the distribution of new fixated bases; IV) the hypothesis of the neighbor influence on the mutation rates in a site. The expected random number of fixations per site was estimated by Bose-Einstein statistics, and the expected frequencies of bases by matrices of mutation-fixation rates. The homogeneity of new fixations was analyzed using χ² and trinomial tests for homogeneity. Fixations of the central base in trinucleotides were used to test the neighbor influence on base substitutions. Neither the number of fixations nor the frequencies of bases fitted the expected neutral distribution. There was a highly significant heterogeneity in the distribution of new fixations, and several sites showed more transversions than transitions, showing that each nucleotide site has its own pattern of change. These three independent results make the neutral theory, the nearly neutral and the neighbor influence hypotheses untenable and indicate that evolution of env is rather highly selective.

Phylogenetic relationships among tribes in Xylocopinae (Apidae) and implications on nest structure evolution.

The subfamily Xylocopinae has been recognized as the most basal lineage within the family Apidae, comprising four tribes; Allodapini, Ceratinini, Xylocopini and Manueliini. Relationships among the tribes are not well resolved with morphological data. In particular, Manueliini and Xylocopini have each been placed as the most basal lineage in separate analyses of the subfamily. While relationships within each tribe, excepting Manueliini, have been investigated using molecular data, these data have not been applied to examine the relationships among tribes, which remain controversial. Here we present results of molecular phylogenetic analyses using sequences of CoI, Cytb and EF-1alphaF1 from members of the four tribes of Xylocopinae. We used available data from other studies in combination with data generated for the three species of Manueliini. Competing phylogenetic hypotheses regarding the alternate positions proposed to Manueliini and Xylocopini were evaluated through statistical tests. The basal position of either Manueliini or Xylocopini has contrasting implications on the evolutionary history of nest architecture, which mediates the potential for contact between adult and immature individuals. Our results indicate that Manueliini is the most basal lineage of Xylocopinae, in agreement with an evolutionary transition from nests having completely sealed cells to nests lacking cells. A nest structure with closed cells prevents physical interactions between adult and immature stages, whereas an open structure provides the opportunity for interactions that may play an important role in the emergence of sociality.

Fixations of the HIV-1 env gene refute neutralism: New evidence for pan-selective evolution

We examined 103 nucleotide sequences of the HIV-1 env gene, sampled from 35 countries and tested: I) the random (neutral) distribution of the number of nucleotide changes; II) the proportion of bases at molecular equilibrium; III) the neutral expected homogeneity of the distribution of new fxated bases; IV) the hypothesis of the neighbor infuence on the mutation rates in a site. The expected random number of fxations per site was estimated by Bose-Einstein statistics, and the expected frequencies of bases by matrices of mutation-fxation rates. The homogeneity of new fxations was analyzed using χ2 and trinomial tests for homogeneity. Fixations of the central base in trinucleotides were used to test the neighbor infuence on base substitutions. Neither the number of fxations nor the frequencies of bases ftted the expected neutral distribution. There was a highly signifcant heterogeneity in the distribution of new fxations, and several sites showed more transversions than transitions, showing that each nucleotide site has its own pattern of change. These three independent results make the neutral theory, the nearly neutral and the neighbor infuence hypotheses untenable and indicate that evolution of env is rather highly selective.